Changes in version 1.4.0.9000                      

This is a list of changes made in the development/GitHub version of the
package between bioregion 1.4.0 (CRAN release 2026-03-29) and the next
CRAN release.

  - Relaxed matching controls in site_species_metrics() and
    bioregion_metrics().

                 Changes in version 1.4.0 (2026-03-29)                  

This is a list of changes made between bioregion 1.3.0 (CRAN
release 2026-01-23) and bioregion 1.4.0 (CRAN release 2026-03-29).

  - bioregion_metrics() has been updated. It now supports multiple
    bioregion
    partitions and spatial coherence can be computed using either the
    size or
    the area of the largest contiguous component. The col_bioregion
    argument
    is now deprecated.

  - map_bioregion() has been reformatted: bioregionalization argument
    changed to partition_index, clusters to bioregionalization, geometry
    to map and write_clusters to map_as_output.

  - map_bioregion() can now handle terra inputs (terra added in
    Suggests).

  - clusters argument changed to bioregionalization in
    site_species_subset().

  - Added seed argument to hclu_hierarclust() (issue #10).

  - Fixed invalid input, control and output in nhclu_affprop() (issue
    #14).

                 Changes in version 1.3.0 (2026-01-23)                  

This is a list of changes made between bioregion 1.2.0 (CRAN
release 2025-01-31) and bioregion 1.3.0 (CRAN release 2026-01-23).

Function changes

  - Added the inputs$data_type field to all clustering outputs to
    explicitly track whether original co-occurrence data were
    occurrence-based or abundance-based. This field is automatically
    determined based on the algorithm type and the
    similarity/dissimilarity metric used.

  - Added the inputs$node_type field to all clustering outputs to
    explicitly indicate whether the clustering includes only sites or
    both sites and species. This changes include the hidden node_type
    attributes.

  - site_species_metrics() has been thoroughly reformatted and now
    provides: species-per-bioregions metrics,
    species-in-bioregionalization metrics, site-per-chorotypes metrics,
    site-in-chorological classification metrics, site-per-bioregions
    metrics, and site-in-bioregionalization metrics, all of which are
    rigorously defined in the corresponding vignette.

  - site_species_subset() has been simplified taking advantage on
    inputs$node_type.

  - Renamed the class bioregion.pairwise.metric to bioregion.pairwise.

  - Added a verbose argument to all talkative functions allowing users
    to control the display of progress messages.

New features

  - Added export of the function exportGDF() with documentation and
    tests.

  - Added bioregion_colors() to provide consistent bioregion color
    palettes for use across multiple visualizations (maps, networks,
    graphs, etc.).

  - Updated map_bioregions() to handle bioregion colors.

  - Added a generic function summary() for a clearer display of results.

  - Added bind_pairwise() to combine pairwise (dis)similarity objects.

  - Added as_bioregion_pairwise() to replace and improve upon
    betapart_to_bioregion(), which is now deprecated.

  - Added a comparison with other R packages for computing dissimilarity
    metrics in tutorial 3 (Pairwise similarity/dissimilarity metrics).

Bug fixes

  - Fixed an tibble input problem with net_to_mat() (issue #11).

  - Fixed a problem in inputs$pairwise_metric when numeric index in all
    clustering outputs.

  - Modified the keep_trials argument in hclu_hierarclust() and fixed a
    potential issue with randomized matrix storage.

                 Changes in version 1.2.0 (2025-01-31)                  

This is a list of changes made between bioregion 1.1.1 (CRAN
release 2024-04-19) and bioregion 1.2.0 (CRAN release 2025-01-31).

  - Added affinity propagation algorithm (nhclu_affprop()).

  - Added a new method in hclu_hierarclust() to construct a consensus
    tree called Iterative Hierarchical Consensus Tree (IHCT). This
    resolves issues related to the order of sites in the distance matrix
    and builds a consensus hierarchical tree with meaningful topology.

  - Made many changes to functions related to hclu_hierarclust() due to
    this major update.

  - Updated generic functions to provide plot and print methods for
    hclu_diana().

  - Added site_species_metrics() to the package and workflow.

  - Added bioregion_metrics() to the package and workflow.

  - Renamed subset_node() to site_species_subset().

  - Added indices Cz to site_species_metrics().

  - Updated install_binaries():
    
      - Archive bin.zip now stored on GitHub and backed up on NextCloud.
      - Added Infomap version 2.8.0.
      - Added argument download_only to execute only the download step.
         

  - Added check_install argument to netclu_infomap(), netclu_louvain(),
    and netclu_oslom().

  - Added betapart_to_bioregion() to the package.

  - Added compare_bioregionalizations() to the package.

  - Added bioregionalization_metrics() to the package.

  - Updated documentation, vignettes, and tests.

  - Modified the way seeds are generated for nhclu_clara() and
    nhclu_clarans().

                 Changes in version 1.1.1 (2024-04-19)                  

This is a list of changes made between bioregion 1.1.0 (CRAN
release 2024-03-19) and bioregion 1.1.1 (CRAN release 2024-04-19).

  - Added hierarchy support for Louvain (C++).

  - Added seed argument to stochastic algorithms (except Louvain C++).

  - Added cut_weight argument to netclu_* functions.

  - Changed value for sites without clusters from 0 to NA.

  - Updated automated tests (code coverage > 60%).

  - Standardized controls, inputs, and outputs.

  - Fixed a bug in find_optimal_n() for cases where partition metrics
    did not vary.

                 Changes in version 1.1.0 (2024-03-19)                  

This is a list of changes made between bioregion 1.0.0 (CRAN
release 2023-04-15) and bioregion 1.1.0 (CRAN release 2024-03-19).

  - Added the resolution parameter to the igraph Louvain implementation.

  - Added options to mat_to_net() to exclude diagonal and lower
    triangular matrices using include_diag and include_lower.

  - Added a function to extract a subset of nodes (sites or species)
    from bioregion.clusters objects containing both types.

  - Added a generic function to maintain attributes of
    bioregion.pairwise objects and track the number of sites and
    species.

  - Added new functions: nhclu_clara() and nhclu_clarans().

  - Edited vignettes to document new functions.

  - Modified controls for bioregion.pairwise objects.

  - Added the include_formula argument to
    similarity_dissimilarity_conversion() to (not) select formula
    metrics.

  - Allowed negative values in similarity() with the Euclidean metric.

                 Changes in version 1.0.0 (2023-04-14)                  

First release on CRAN